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Introduction

Welcome to your QCeltis Quality Control Analysis Report! We are pleased to present to you a visual QC summary of your dataset. Representing high-dimensional omics data using plots helps us view large amounts of information at once to identifying patterns and trends across your samples and datasets. The QCeltis package monitors metrics based on the input datasets provided. For any concerns about or suggestions to improve this report, let the team know at GroupHeartBioinformaticsSupport@cshs.org, and we will consider your feedback. We are happy to support your computational needs.

The report is divided into 2 tabs:

  • ID-Free - When a mzML directory is provided as input, ID-Free Tab is populated with plots from ID-Free parameters extracted from your mzML files.
  • ID-Based - When a protein, peptide or precursor level intensity file is provided, ID-based Tab will be populated with ID-based parameters extracted from your quantified input.

ID-Free Metrics

The following ID-Free metrics have been extracted from the provided mzML files. Given thresholds have been applied and outlier analysis has been performed. If no outliers were found, outlier plots will not be plotted. If a grouping file was provided, additional groupwise plots will be included.

Total Ion Current

The total ion current (TIC) is the summed intensity across the entire range of masses being detected in each sample. MS1 and MS2 Total Ion Current Values extracted from spectra within the given mzML files

TIC Outliers

MS1 TIC is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition and LC-MS instrument performance such as improper autosampler sample pickup. Please check the specific samples listed below.

1 outliers were found. The following files have been detected as outliers: 20220103_AMP-PD_P-17_DepPlasma_PD_DR_Rep_2_profile.mzML

Groupwise TIC CV%

When a grouping file is provided, CV% for TIC values across samples in each group is calculated. This provides an insignt into how consistent the samples are within each group.

CV% for MS1 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold

CV% for MS2 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold


Spectral Ratio

The number of spectra recorded in each mzML file is extracted. The spectral ratio represents the number of MS2 Spectra over the number of MS1 Spectra found in each file.

Max Base Peak Intensity

The base peak intensity is the recorded intensity of the most intense peak from each spectrum in the mzML file. The Max Base Peak Intensity represents the highest recorded base peak intensity in each mzML file.

ID-Based Metrics

The following ID-Based metrics have been calculated and derived from the input search results that were provided. Given input thresholds have been applied and if grouping file was provided, additional groupwise plots will be included.


Protein Quantification

Number of proteins identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation, digestion protocols or experimental reproducibility.

Peptide Quantification

Number of peptides identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation, digestion protocols or experimental reproducibility.


Intensity CV% Cumulative Frequency

Cumulative Frequency % of calculated CV% of intensity values across all samples. This reveals the degree of variability across the dataset, higher CVs indicate greater variation that could be stemming from sample preparation, data acquisition or instrument performance. Lower CVs indicate higher reproducibility of protein, peptide or precursor intensities across replicate samples.

Percentage of Proteins Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 50.0% of proteins under 30.0 CV%. This provides information about the consistency and reproducibility of intensity values within each provided group. Any groups not meeting the threshold indicate batch or plate-specific issues that need to be looked into.

Percentage of Peptides Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 50.0% of peptides under 30.0 CV%. This provides information about the consistency and reproducibility of intensity values within each provided group. Any groups not meeting the threshold indicate batch or plate-specific issues that need to be looked into.


PCA for Protein Intensities

PCA plot from protein intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.

PCA for Peptide Intensities

PCA plot from peptide intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.


Common Peptide TIC

The Total Ion Current here is calculated from intensities of common peptides found in all samples. Any inconsistent patterns could indicate problems in sample preparation.

Common Peptide TIC Group CV%

Common Peptide TIC CV% calculated from intensities of common peptides within each provided group. A CV% higher than the set threshold of 30.0 indicates an inconsistency within the samples of the group


No Miscleavages Percentage

Total Number of 0 miscleaved peptides found in each sample. If the percentage of 0 miscleaved peptides is under the miscleavage threshold value of 60.0%, this could indicate issues with sample preparation and digestion protocols.


iRT Intensity Distribution

iRT intensity distribution across all provided samples. The intensity values are expected to be consistent across replicate quality control samples. High intensity values for specific samples could indicate double-spiking of iRTs, low intensity values could indicate issues with proper sample preparation.

iRT Peptides Coverage across all samples. Each bar represents the percentage of samples that each iRT Peptide is present in.